4IN3 | pdb_00004in3

Crystal Structure of the Chs5-Bch1 Exomer Cargo Adaptor Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 
    0.289 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

The exomer cargo adaptor features a flexible hinge domain.

Richardson, B.C.Fromme, J.C.

(2013) Structure 21: 486-492

  • DOI: https://doi.org/10.1016/j.str.2013.01.003
  • Primary Citation Related Structures: 
    4IN3

  • PubMed Abstract: 

    Exomer is a cargo adaptor that mediates the sorting of specific plasma membrane proteins into vesicles at the trans-Golgi network. Cargo adaptors must bind to multiple partners, including their cargo, regulatory proteins, and the membrane surface. During biogenesis of a vesicle, the membrane makes a transition from a relatively flat surface to one of high curvature, requiring cargo adaptors to somehow maintain protein-protein and protein-membrane interactions on a changing membrane environment. Here, we present the crystal structure of a tetrameric Chs5/Bch1 exomer complex and use small-angle X-ray scattering to demonstrate its flexibility in solution. The structural data suggest that the complex flexes primarily around the dimeric N-terminal domain of the Chs5 subunits, which adopts a noncanonical β sandwich fold. We propose that this flexible hinge domain enables exomer to maintain interactions in the context of a dynamic membrane environment.


  • Organizational Affiliation
    • Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.

Macromolecule Content 

  • Total Structure Weight: 186.49 kDa 
  • Atom Count: 11,087 
  • Modeled Residue Count: 1,376 
  • Deposited Residue Count: 1,642 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chitin biosynthesis protein CHS5
A, C
82Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CHS5CAL3YLR330WL8543.18
UniProt
Find proteins for Q12114 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12114 
Go to UniProtKB:  Q12114
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12114
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein BCH1
B, D
739Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: BCH1YMR237WYM9959.19
UniProt
Find proteins for Q05029 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05029 
Go to UniProtKB:  Q05029
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05029
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free:  0.289 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.391α = 90
b = 155.686β = 95.34
c = 99.054γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description